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RBPmotif specifications


Unique identifier OMICS_03826
Name RBPmotif
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for RBPmotif

RBPmotif citations


RNA Binding Protein Vigilin Collaborates with miRNAs To Regulate Gene Expression for Caenorhabditis elegans Larval Development

PMCID: 5555458
PMID: 28576776
DOI: 10.1534/g3.117.043414

[…] miRNAs and families of miRNAs in regulating the first larval stage of C. elegans development.Although we were not able to determine a high confidence VGLN-1 binding motif using computational methods [RBPMotif ()], the enrichment of specific miRNA target sites among VGLN-1 target mRNAs could suggest that alternative methods of functional selectivity may exist. This enrichment and genetic interactio […]


Revealing protein–lncRNA interaction

Brief Bioinform
PMCID: 4719072
PMID: 26041786
DOI: 10.1093/bib/bbv031

[…] context of motif discovery at RBP binding sites can be found in []. The already mentioned MEMERIS [], CMfinder [], RNApromo [], StructRED [], the algorithm by Li and collaborators [], RNAcontext and RBPmotif [, ], GraphProt [] and Zagros [] are all tools that use, with different strategies and to different extent, secondary structure information to determine more specific binding motifs.The appli […]


High throughput characterization of protein–RNA interactions

Brief Funct Genomics
PMCID: 4303715
PMID: 25504152
DOI: 10.1093/bfgp/elu047

[…] condary structure context (e.g. a hairpin loop) and learns the weights for each position from a set of input sequences annotated with relative binding affinity []. RNAcontext is also available on the RBPmotif Web server [].The second approach considers RNA secondary structure explicitly and includes stochastic context-free grammar (SCFG) and graphical approaches. CMfinder [] and RNApromo [] both s […]


Finding the target sites of RNA binding proteins

PMCID: 4253089
PMID: 24217996
DOI: 10.1002/wrna.1201

[…] binding affinities of the RBP of interest. Each input RNA sequence is scored by using the sequence and structure context parameters. RNAcontext has been applied to in vitro binding-affinity data. The RBPmotif webserver implements RNAcontext. […]


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RBPmotif institution(s)
Department of Computer Engineering, Antalya International University, Antalya, Turkey

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